[English] 日本語
Yorodumi
- PDB-4c9l: Structure of Cyanide and Camphor bound wild type CYP101D1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c9l
TitleStructure of Cyanide and Camphor bound wild type CYP101D1
ComponentsCYTOCHROME P450
KeywordsOXIDOREDUCTASE / MONO-OXYGENASE
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / membrane
Similarity search - Function
Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CAMPHOR / CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesNOVOSPHINGOBIUM AROMATICIVORANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsBatabyal, D. / L Poulos, T.
CitationJournal: Biochemistry / Year: 2013
Title: Crystal Structures and Functional Characterization of Wild Type and Active Sites Mutants of Cyp101D1.
Authors: Batabyal, D. / Poulos, T.L.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Atomic model
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CYTOCHROME P450
B: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2658
Polymers94,6762
Non-polymers1,5896
Water17,583976
1
A: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1334
Polymers47,3381
Non-polymers7953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CYTOCHROME P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1334
Polymers47,3381
Non-polymers7953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)151.529, 151.529, 196.041
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-2142-

HOH

-
Components

#1: Protein CYTOCHROME P450 / CYP101D1


Mass: 47337.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NOVOSPHINGOBIUM AROMATICIVORANS (bacteria)
Strain: DSM12444 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2GB12
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#4: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 976 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.43 Å3/Da / Density % sol: 64.15 % / Description: NONE
Crystal growpH: 8.2 / Details: 100MM TRIS PH 8.2, 1.6M AMMONIUM SULPHATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→49.6 Å / Num. obs: 121806 / % possible obs: 99.7 % / Observed criterion σ(I): 4.4 / Redundancy: 9.4 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.4
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 4.4 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LXI

3lxi


Resolution: 1.801→46.301 Å / SU ML: 0.14 / σ(F): 1.33 / Phase error: 16.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1825 1999 1.6 %
Rwork0.152 --
obs0.1525 121658 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→46.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6471 0 112 976 7559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116765
X-RAY DIFFRACTIONf_angle_d1.4029232
X-RAY DIFFRACTIONf_dihedral_angle_d14.5932516
X-RAY DIFFRACTIONf_chiral_restr0.097993
X-RAY DIFFRACTIONf_plane_restr0.0071202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.8460.24111400.18118383X-RAY DIFFRACTION99
1.846-1.89590.2291390.1648379X-RAY DIFFRACTION99
1.8959-1.95170.21561410.16298423X-RAY DIFFRACTION99
1.9517-2.01470.17441410.14828434X-RAY DIFFRACTION99
2.0147-2.08670.17741410.14238443X-RAY DIFFRACTION99
2.0867-2.17030.16221420.148454X-RAY DIFFRACTION99
2.1703-2.26910.16241410.13668479X-RAY DIFFRACTION100
2.2691-2.38870.16971420.13978512X-RAY DIFFRACTION100
2.3887-2.53830.18841430.1438535X-RAY DIFFRACTION100
2.5383-2.73430.19271440.15488571X-RAY DIFFRACTION100
2.7343-3.00940.19561430.15948590X-RAY DIFFRACTION100
3.0094-3.44480.17721440.15798676X-RAY DIFFRACTION100
3.4448-4.33950.16651470.14328727X-RAY DIFFRACTION100
4.3395-46.31670.18711510.16319053X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7008-0.3690.00140.97510.08550.4717-0.01860.02970.0082-0.06820.0092-0.0557-0.05490.11080.00740.0768-0.0234-0.01510.1595-0.00920.093434.991117.58143.9067
20.93650.0847-0.05150.5390.10020.69380.03010.07260.0495-0.0909-0.00750.1224-0.1941-0.1146-0.03170.16860.0246-0.04610.1630.01210.138411.386830.52733.1616
30.91620.13480.14961.7184-0.28071.2703-0.01830.13930.229-0.05920.0305-0.0938-0.26530.2485-0.01660.2262-0.0575-0.02680.21240.03280.172127.590439.1342-5.5514
40.9309-0.3284-0.00830.65860.04210.6229-0.0679-0.0789-0.05180.02460.05620.0729-0.0801-0.01530.01560.0840.0054-0.01850.1421-0.00130.092620.419621.067712.3389
51.5383-0.5608-0.15950.71670.05250.1915-0.0435-0.07430.03060.02450.036-0.0546-0.01690.0420.02130.0890.0082-0.00310.22290.00610.116151.283512.00834.4545
61.8715-0.0379-0.33270.68260.01431.20180.0293-0.330.30360.0502-0.013-0.1985-0.15310.1560.02760.1026-0.0136-0.04550.29780.01420.24666.996518.419336.5589
71.3378-0.50090.00850.8669-0.22440.4798-0.01870.0437-0.1333-0.06020.02060.01720.04720.0237-0.00480.04610.00920.00090.16620.0090.091547.78766.648629.2466
81.1606-0.47480.06611.13490.53451.0663-0.0873-0.1228-0.40020.16540.09370.10970.20170.06190.00670.10240.04250.02730.23180.05650.26155.4968-6.972636.919
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 10 THROUGH 122 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 123 THROUGH 193 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 194 THROUGH 242 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 243 THROUGH 417 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 11 THROUGH 172 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 173 THROUGH 242 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 243 THROUGH 367 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 368 THROUGH 417 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more